Nature Microbiology最新文献_第3页

A single-cell atlas of Toxoplasma sexual development in the feline intestinal tract. 猫肠道内弓形虫性发育的单细胞图谱。

IF 28.3 1区生物学

Nature Microbiology Pub Date : 2026-04-22 DOI: 10.1038/s41564-026-02294-7

Hisham S Alrubaye,Sarah M Reilly,Rafaela da Silva,NyJaee Washington,Jon P Boyle

引用次数: 0

Benchmarking of shotgun sequencing depth reveals the potential and limitations of shallow metagenomics and strain-level analysis. 霰弹枪测序深度的基准分析揭示了浅层宏基因组学和菌株水平分析的潜力和局限性。

IF 28.3 1区生物学

Nature Microbiology Pub Date : 2026-04-21 DOI: 10.1038/s41564-026-02334-2

Nicole S Treichel,Charlie Pauvert,Joana Séneca,Petra Pjevac,David Berry,John Penders,Thomas C A Hitch,Thomas Clavel

{"title":"Benchmarking of shotgun sequencing depth reveals the potential and limitations of shallow metagenomics and strain-level analysis.","authors":"Nicole S Treichel,Charlie Pauvert,Joana Séneca,Petra Pjevac,David Berry,John Penders,Thomas C A Hitch,Thomas Clavel","doi":"10.1038/s41564-026-02334-2","DOIUrl":"https://doi.org/10.1038/s41564-026-02334-2","url":null,"abstract":"Shotgun metagenomics can provide both taxonomic and functional insights, but benchmarking is necessary to determine the sequencing depth appropriate for specific analyses. Here we used complex mixtures of DNA from cultured bacteria and analysed taxonomic composition, strain-level resolution and functional profiles at up to 11 sequencing depths (0.1-50.0 Gb). Reference-based analysis provided accurate strain-level taxonomy at 0.5-1.0 Gb. By contrast, de novo metagenome-assembled genome (MAG) reconstruction required deep sequencing (>10 Gb), and even MAGs deemed high quality by standard metrics were chimeric, with 54.5-81.8% accurately representing original strains, depending on the bioinformatic approach. Functionally, 2 Gb provided reliable insights at the pathway level for each of the mock communities tested, but sufficient proteome coverage was achieved only at or above 10 Gb. Library preparation and host DNA contamination were identified as confounders in shallow metagenomic analysis. This analysis highlights the potential and limitations of shallow metagenomics and provides guidance to accurately capture strain-level diversity using MAGs.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"46 1","pages":""},"PeriodicalIF":28.3,"publicationDate":"2026-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147731400","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Navigating multi-omic integration methods for human microbiome research. 导航人类微生物组研究的多组学整合方法。

IF 28.3 1区生物学

Nature Microbiology Pub Date : 2026-04-21 DOI: 10.1038/s41564-026-02328-0

Efrat Muller,Tal Bamberger,Elhanan Borenstein

{"title":"Navigating multi-omic integration methods for human microbiome research.","authors":"Efrat Muller,Tal Bamberger,Elhanan Borenstein","doi":"10.1038/s41564-026-02328-0","DOIUrl":"https://doi.org/10.1038/s41564-026-02328-0","url":null,"abstract":"Multi-omic studies in human microbiome research hold great potential for advancing our understanding of host-microbiome interactions. However, despite the growing availability of multi-omic datasets, analysing such data remains a major conceptual, analytical and computational challenge. Introduction of new multi-omic integration methods to address these challenges further complicates researchers' efforts to navigate this expanding field. In this Review, we outline the landscape of multi-omic integration methods in the context of human microbiome research. In contrast to previous reviews, we specifically emphasize the different biological questions addressed by various integration approaches, including questions related to interactions between different molecular layers, molecular shifts that occur in disease, subgrouping of patients based on molecular profiles, and identification of biological mechanisms that underlie such associations. Our aim is to provide a timely, convenient and comprehensive resource for the microbiome research community, allowing researchers to identify the multi-omic integration approach that is best suited to their data and objectives.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"24 1","pages":""},"PeriodicalIF":28.3,"publicationDate":"2026-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147731333","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

When viral RNA lingers in joints. 当病毒RNA在关节中徘徊时。

IF 28.3 1区生物学

Nature Microbiology Pub Date : 2026-04-21 DOI: 10.1038/s41564-026-02332-4

Clive S McKimmie,Marieke Pingen

引用次数: 0

Phytophthora targets plant extracellular vesicles to promote infection. 疫霉菌以植物细胞外囊泡为目标，促进感染。

IF 28.3 1区生物学

Nature Microbiology Pub Date : 2026-04-20 DOI: 10.1038/s41564-026-02325-3

Yuanpeng Xu,Xiaoying Kong,Qian Qiao,Changhao Liu,Jinyi Zhu,Lei Wang,Yanhao Hu,Yujing Sun,Min Qiu,Wei Yan,Suomeng Dong,Wenbo Ma,Yan Wang,Yuanchao Wang

{"title":"Phytophthora targets plant extracellular vesicles to promote infection.","authors":"Yuanpeng Xu,Xiaoying Kong,Qian Qiao,Changhao Liu,Jinyi Zhu,Lei Wang,Yanhao Hu,Yujing Sun,Min Qiu,Wei Yan,Suomeng Dong,Wenbo Ma,Yan Wang,Yuanchao Wang","doi":"10.1038/s41564-026-02325-3","DOIUrl":"https://doi.org/10.1038/s41564-026-02325-3","url":null,"abstract":"Extracellular vesicles (EVs) transport biologically active molecules and are known to mediate host defence against microbial pathogens, including plant fungal pathogens. However, the mechanism by which pathogens disrupt EV-dependent defence remains unclear. Here we show that Phytophthora capsici, a global crop pathogen, counteracts EV-mediated plant defence through targeted lipase activity. We show that Arabidopsis releases EVs containing tetraspanin (TET), specifically TET8- and TET9-EVs, which damage germinated spores of Phytophthora, reducing infection. As a counter-defence, Phytophthora secretes an infection-induced apoplastic lipase, Plant Extracellular Vesicle Destroyer 1 (PED1), which targets TET8- and TET9-EVs. This occurs via interaction with the EV membrane-localized protein Defective Glycosylation 1 (DGL1), which directly interacts and co-localizes with TET8 and TET9 on the EV membrane. PED1 damages TET8- and TET9-EVs through its lipase activity towards campesteryl esters, suppressing EV-mediated plant defence. Our study reveals a mechanism used by Phytophthora to counteract EV-mediated host defence.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"136 1","pages":""},"PeriodicalIF":28.3,"publicationDate":"2026-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147726220","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

MoCox6 is a regulator of mitophagy and a druggable target in Magnaporthe oryzae. MoCox6是一种线粒体自噬的调节因子，是稻谷菌的一个可药物靶点。

IF 28.3 1区生物学

Nature Microbiology Pub Date : 2026-04-20 DOI: 10.1038/s41564-026-02329-z

Ming-Hua Wu,Ya-Nan Lv,Hui Li,Hui Qian,Yun-Yun Wei,Yun-Ran Zhang,Shuang Liang,Xue-Ming Zhu,Jian-Ping Lu,Maurizio Del Poeta,Zong-Hua Wang,Yong-Hwan Lee,Naweed I Naqvi,Richard A Wilson,Daniel J Klionsky,Fu-Cheng Lin,Xiao-Hong Liu

{"title":"MoCox6 is a regulator of mitophagy and a druggable target in Magnaporthe oryzae.","authors":"Ming-Hua Wu,Ya-Nan Lv,Hui Li,Hui Qian,Yun-Yun Wei,Yun-Ran Zhang,Shuang Liang,Xue-Ming Zhu,Jian-Ping Lu,Maurizio Del Poeta,Zong-Hua Wang,Yong-Hwan Lee,Naweed I Naqvi,Richard A Wilson,Daniel J Klionsky,Fu-Cheng Lin,Xiao-Hong Liu","doi":"10.1038/s41564-026-02329-z","DOIUrl":"https://doi.org/10.1038/s41564-026-02329-z","url":null,"abstract":"Mitophagy is a selective autophagic process that maintains cellular homeostasis by degrading damaged mitochondria and is a promising antifungal target. However, few inner mitochondrial membrane (IMM) regulators of mitophagy are known. Here we identify cytochrome c oxidase subunit 6 (MoCox6) as an IMM regulator in Magnaporthe oryzae that binds MoAtg5 and MoAtg14 following outer mitochondrial membrane rupture to mediate mitophagy. MoSirt5 regulates this process by desuccinylating MoCox6 at K144. Structural analysis revealed that residue D95 at the MoSirt5-MoCox6 interface mediates the dual role of MoCox6 in mitophagy and mitochondrial metabolic competence. Deletion of the COX6 gene significantly reduced vegetative growth and virulence in both M. oryzae and Alternaria alternata. Through high-throughput screening, we identified a small-molecule compound, Pan-RAS-IN-1, which targets MoCox6 to inhibit mitophagy, thereby suppressing M. oryzae virulence. Pan-RAS-IN-1 exhibits broad-spectrum antifungal activity, and its application to rice plants significantly suppressed rice blast incidence.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"16 1","pages":""},"PeriodicalIF":28.3,"publicationDate":"2026-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147726222","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A boron-based agent to treat multidrug-resistant gonorrhoea. 一种硼基药剂，用于治疗多重耐药淋病。

IF 28.3 1区生物学

Nature Microbiology Pub Date : 2026-04-20 DOI: 10.1038/s41564-026-02330-6

引用次数: 0

Salmonella-derived haem inhibits macrophage phagocytosis and promotes infection in mice. 沙门氏菌来源的血红素抑制巨噬细胞吞噬并促进小鼠感染。

IF 28.3 1区生物学

Nature Microbiology Pub Date : 2026-04-20 DOI: 10.1038/s41564-026-02341-3

Zuoqiang Wang,Huang Tang,Wanqiu Huang,Chengyue Wang,Yana Chen,Jingchen Yu,Tao Zhou,Bingjie Wen,Jinjing Ni,Danni Wang,Jing Tao,Siqi Zhu,Lin Lyu,Lei Chen,Jun Li,Qihong Kuang,Daojin Yu,Jianping Liu,Lifeng Pan,Mei Zhang,Yue Xu,Guo-Ping Zhao,Jie Lu,Yu-Feng Yao

{"title":"Salmonella-derived haem inhibits macrophage phagocytosis and promotes infection in mice.","authors":"Zuoqiang Wang,Huang Tang,Wanqiu Huang,Chengyue Wang,Yana Chen,Jingchen Yu,Tao Zhou,Bingjie Wen,Jinjing Ni,Danni Wang,Jing Tao,Siqi Zhu,Lin Lyu,Lei Chen,Jun Li,Qihong Kuang,Daojin Yu,Jianping Liu,Lifeng Pan,Mei Zhang,Yue Xu,Guo-Ping Zhao,Jie Lu,Yu-Feng Yao","doi":"10.1038/s41564-026-02341-3","DOIUrl":"https://doi.org/10.1038/s41564-026-02341-3","url":null,"abstract":"Bacterial pathogens such as Salmonella enterica serovar Typhimurium can resist phagocytosis by macrophages. Here we explored the role of bacterial haem biosynthesis in phagocytosis resistance. Using transposon sequencing (Tn-seq) during Salmonella infection of macrophages, we identify a methyltransferase, SirM, that indirectly inhibits phagocytosis of bacteria. Mechanistically, sirM is activated upon interaction with macrophages and methylates HemL, a key enzyme in haem biosynthesis, resulting in upregulation of haem synthesis by Salmonella. Salmonella-derived haem inhibits Cdc42 activation in a Toll-like receptor 4 (TLR4)-dependent manner to inhibit phagocytosis. Moreover, sirM promotes macrophage death by increasing haem synthesis. Experiments in mouse models show that sirM is required for virulence and confers a competitive advantage over intestinal commensal bacteria during infection. We also found that sirM is distributed among enteric pathogens. Collectively, our findings show that bacterial haem promotes evasion of phagocyte responses and pathogenesis to confer an advantage in the host.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"73 1","pages":""},"PeriodicalIF":28.3,"publicationDate":"2026-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147726221","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Hunting for new lineages and mechanisms of life. 寻找新的血统和生命机制。

IF 28.3 1区生物学

Nature Microbiology Pub Date : 2026-04-20 DOI: 10.1038/s41564-026-02336-0

Gitta Szabó,Eric Olo Ndela,Sujung Lim,Alireza Saidi-Mehrabad,Brian P Hedlund,Frederik Schulz

引用次数: 0

Faecalibacterium prausnitzii enzyme reprograms PD-L1 trafficking and sensitizes colorectal cancer to immunotherapy in mice. prausnitzii Faecalibacterium酶重编程PD-L1运输并使小鼠结直肠癌对免疫治疗敏感。

IF 28.3 1区生物学

Nature Microbiology Pub Date : 2026-04-17 DOI: 10.1038/s41564-026-02326-2

Siqi Ji,Yuanhui Liu,Yuejie Xu,Junzhao Gao,Jingzheng Jin,Ping Jiang,Yixuan Li,Dan Su,Yu Zhao,Shuqiao Yang,Shuai Zhang,Wenbiao Shi,Qian Zhou,Mingming Zhang

{"title":"Faecalibacterium prausnitzii enzyme reprograms PD-L1 trafficking and sensitizes colorectal cancer to immunotherapy in mice.","authors":"Siqi Ji,Yuanhui Liu,Yuejie Xu,Junzhao Gao,Jingzheng Jin,Ping Jiang,Yixuan Li,Dan Su,Yu Zhao,Shuqiao Yang,Shuai Zhang,Wenbiao Shi,Qian Zhou,Mingming Zhang","doi":"10.1038/s41564-026-02326-2","DOIUrl":"https://doi.org/10.1038/s41564-026-02326-2","url":null,"abstract":"Microbiome-host interactions can influence colorectal cancer (CRC) outcomes and the effectiveness of immunotherapy treatment, but the precise mechanisms underlying this are poorly understood. Here we analyse CRC patient cohort data and observe that Facalibacterium prausnitzii abundance in faecal samples correlates with improved CRC survival outcome and immunotherapy response. In vitro assays and experiments in azoxymethane plus dextran sulfate sodium (AOM/DSS) and Apcmin/+ mouse CRC models show that F. prausnitzii extracts have anti-tumour activity. Mass spectrometry identifies F. prausnitzii phosphoribosyl pyrophosphate synthetase (fpPRPS) as a bacterial enzyme that inhibits tumour development and promotes CD8+ T-cell responses. Mechanistically, fpPRPS depletes ATP levels in CRC cells, which then inhibits GTP-GDP exchange on Rab11a, reprogramming CRC energy metabolism. This leads to Rab11a degradation and the disruption of PD-L1 trafficking to reduce the inhibition of T-cell responses. fpPRPS inhibition of tumour progression is PD-L1-dependent. We also show that fpPRPS and anti-PD-1 treatment synergize to promote CD8+ T-cell responses and tumour control in mice. These findings suggest fpPRPS as a potential strategy for sensitizing CRC to immunotherapy.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"19 1","pages":""},"PeriodicalIF":28.3,"publicationDate":"2026-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147702107","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0